Variant report

Variant	rs60367453
Chromosome Location	chr4:152125521-152125522
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:152124247..152127110-chr4:152129155..152131001,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12503016	0.98[ASN][1000 genomes]
rs12504166	0.94[ASN][1000 genomes]
rs12508270	0.88[ASN][1000 genomes]
rs12511209	0.99[ASN][1000 genomes]
rs17633530	0.99[ASN][1000 genomes]
rs17633537	0.99[ASN][1000 genomes]
rs17633600	0.94[ASN][1000 genomes]
rs17633648	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17633654	0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs58496896	0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs59944801	0.91[ASN][1000 genomes]
rs60212468	0.91[ASN][1000 genomes]
rs60761330	0.92[ASN][1000 genomes]
rs60953992	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61442068	0.86[ASN][1000 genomes]
rs6858302	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs72967545	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7671332	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7681468	0.86[ASN][1000 genomes]
rs7699574	0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034948	chr4:151590115-152202687	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv537302	chr4:151590115-152202687	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv530159	chr4:151624865-152203910	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv948719	chr4:151693149-152161625	Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv880262	chr4:151712054-152519899	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
6	nsv881526	chr4:151968295-152489087	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv1016220	chr4:151997139-152164126	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
8	nsv537306	chr4:151997139-152164126	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
9	nsv870229	chr4:152114410-152161072	Genic enhancers Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60367453	RPS3A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152097200-152136600	Weak transcription	Colonic Mucosa	Colon
2	chr4:152097600-152128800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr4:152098400-152147200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr4:152117600-152148800	Weak transcription	Esophagus	oesophagus
5	chr4:152118800-152146600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:152119000-152139400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:152119200-152129000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:152119400-152139400	Weak transcription	NHEK	skin
9	chr4:152120800-152126200	Weak transcription	Spleen	Spleen
10	chr4:152120800-152128200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:152120800-152153800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:152121000-152136400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr4:152121000-152138000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr4:152121200-152133800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr4:152122600-152128000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr4:152123200-152127200	Enhancers	Fetal Stomach	stomach
17	chr4:152123600-152125600	Enhancers	Colon Smooth Muscle	Colon
18	chr4:152123600-152126000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:152123600-152128000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr4:152123600-152128800	Enhancers	Fetal Lung	lung
21	chr4:152123600-152128800	Enhancers	HepG2	liver
22	chr4:152123600-152129200	Enhancers	Brain Hippocampus Middle	brain
23	chr4:152123600-152129400	Enhancers	Brain Substantia Nigra	brain
24	chr4:152124000-152129600	Enhancers	HUVEC	blood vessel
25	chr4:152124200-152126400	Weak transcription	Brain Anterior Caudate	brain
26	chr4:152124400-152126200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:152124400-152126600	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr4:152124400-152126800	Enhancers	A549	lung
29	chr4:152124400-152127400	Weak transcription	NHLF	lung
30	chr4:152124400-152127600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr4:152124400-152128000	Weak transcription	Aorta	Aorta
32	chr4:152124400-152128200	Weak transcription	Lung	lung
33	chr4:152124400-152128800	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:152124400-152129600	Weak transcription	Gastric	stomach
35	chr4:152124400-152136400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr4:152124400-152139600	Weak transcription	Osteobl	bone
37	chr4:152124400-152147000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:152124600-152126000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr4:152124600-152126000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr4:152124600-152126200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr4:152124600-152126400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr4:152124600-152126400	Weak transcription	Fetal Kidney	kidney
43	chr4:152124600-152126400	Weak transcription	Rectal Smooth Muscle	rectum
44	chr4:152124600-152126400	Weak transcription	Right Atrium	heart
45	chr4:152124600-152126400	Weak transcription	Right Ventricle	heart
46	chr4:152124600-152126400	Weak transcription	Stomach Smooth Muscle	stomach
47	chr4:152124600-152128600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr4:152124600-152128800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr4:152124600-152128800	Weak transcription	Pancreas	Pancrea
50	chr4:152124600-152136200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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